Register training material
1561 materials found

Valorisation and intellectual properties in research data management

### Valorisation and IP * Basics of Tech Transfer and IPR from an academic perspective * Insights as to: * Why is it important when handling and managing research data? * How do IP rights fit in FAIR data principles * When to safeguard data for proprietary protection? * Where/how...

Scientific topics: Data management

Keywords: intellectual property protection

Resource type: Presentation

Valorisation and intellectual properties in research data management https://tess.elixir-europe.org/materials/valorisation-and-interlectual-properties-in-research-data-management ### Valorisation and IP * Basics of Tech Transfer and IPR from an academic perspective * Insights as to: * Why is it important when handling and managing research data? * How do IP rights fit in FAIR data principles * When to safeguard data for proprietary protection? * Where/how share and publish data if valorisation is in scope? Data management intellectual property protection life scientists
Preserve, publish and share your data

- why preserve data - what data should be preserved - how share data - where to deposit your data - Fairsharing, re3data - ELIXIR Core Resources - Data Formats - Generic archives

Scientific topics: Data management, Data submission, annotation, and curation

Keywords: data formats, ELIXIR Core resources, FAIR data submission

Resource type: Presentation

Preserve, publish and share your data https://tess.elixir-europe.org/materials/preserve-publish-and-share-your-data - why preserve data - what data should be preserved - how share data - where to deposit your data - Fairsharing, re3data - ELIXIR Core Resources - Data Formats - Generic archives Data management Data submission, annotation, and curation data formats, ELIXIR Core resources, FAIR data submission life scientists
Reusing existing data

- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations

Scientific topics: Data management

Keywords: data licenses, software licenses, data journal

Resource type: Presentation

Reusing existing data https://tess.elixir-europe.org/materials/reusing-existing-data - how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations Data management data licenses, software licenses, data journal life scientists
Organising your data: structure and versioning

how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes

Scientific topics: Data management

Keywords: data stewardship, data collection

Resource type: Presentation

Organising your data: structure and versioning https://tess.elixir-europe.org/materials/organising-your-data-structure-and-versioning how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes Nele Pauwels Data management data stewardship, data collection
FAIRify your data: data documentation and metadata

“Documentation is a love letter that you write to your future self.” Damian Conway (2005) Make your data as useful as possible for “your future self” and others Never forget what you did or how or why you did it Always find beck your precious data (easily) Make data understandable,...

Scientific topics: Data management

Keywords: data documentation, metadata

Resource type: Presentation

FAIRify your data: data documentation and metadata https://tess.elixir-europe.org/materials/fairify-your-data-data-documentation-and-metadata “Documentation is a love letter that you write to your future self.” Damian Conway (2005) Make your data as useful as possible for “your future self” and others Never forget what you did or how or why you did it Always find beck your precious data (easily) Make data understandable, reproducible and reusable by “your future self” and others Avoid misinterpretation Data management data documentation, metadata life scientists
Data Management Plans

dmponline.be - creating data management plans why, what to cover, examples and self-assessment grids

Keywords: Data management planning

Resource type: Presentation

Data Management Plans https://tess.elixir-europe.org/materials/data-management-plans dmponline.be - creating data management plans why, what to cover, examples and self-assessment grids Data management planning life scientists
Privacy and GDPR in the research life cycle

0. The basics 1. Planning your research from a GDPR point of view 2. From planning to collecting your data 3. Structuring and analyzing your data 4. Sharing, publishing, archiving and destroying your data

Scientific topics: Data management

Keywords: GDPR

Resource type: Presentation

Privacy and GDPR in the research life cycle https://tess.elixir-europe.org/materials/privacy-and-gdpr-in-the-research-life-cycle 0. The basics 1. Planning your research from a GDPR point of view 2. From planning to collecting your data 3. Structuring and analyzing your data 4. Sharing, publishing, archiving and destroying your data Data management GDPR life scientists
Research Data Management: Trends and requirements

Paula Oset - Research funders and journal policies

Scientific topics: Data management

Keywords: journal policies, research funding

Resource type: Presentation

Research Data Management: Trends and requirements https://tess.elixir-europe.org/materials/research-data-management-trends-and-requirements Paula Oset - Research funders and journal policies Data management journal policies, research funding life scientists
Introduction to Research Data Management and the data life cycle

RESEARCH DATA MANAGEMENT IN LIFE SCIENCES Introduction to RDM & data lifecycle Thomas Van de Velde (Data steward team Ghent University)

Keywords: research data, data management

Resource type: Presentation

Introduction to Research Data Management and the data life cycle https://tess.elixir-europe.org/materials/introduction-to-research-data-management-and-the-data-life-cycle RESEARCH DATA MANAGEMENT IN LIFE SCIENCES Introduction to RDM & data lifecycle Thomas Van de Velde (Data steward team Ghent University) research data, data management life scientists
Slides from Data Management Planning Workshop

Slides from Data Management Planning online workshop for Life Science Projects for researchers at NTNU 2020-12-01

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop https://tess.elixir-europe.org/materials/slides-from-data-management-planning-workshop-08010d67-d503-436b-95b9-6fe29f47ebba Slides from Data Management Planning online workshop for Life Science Projects for researchers at NTNU 2020-12-01 Data management Data management plan, data management PhD students Professors Post Docs All postgraduates
IFB Shiny training

Shiny package training (in french)

Keywords: R-programming, Reproducible Science

IFB Shiny training https://tess.elixir-europe.org/materials/ifb-shiny-training Shiny package training (in french) Hélène Chiapello Jacques van Helden R-programming, Reproducible Science bioinformaticians statisticians
Status Update Code of Conduct: Teaming up & Talking about it

CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR

Keywords: GDPR, Healthcare research, data harmonization

Resource type: Video

Status Update Code of Conduct: Teaming up & Talking about it https://tess.elixir-europe.org/materials/status-update-code-of-conduct-teaming-up-talking-about-it CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR GDPR, Healthcare research, data harmonization
Research Data Management in Life Sciences

The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.

Scientific topics: Data management

Resource type: Presentation, Vignette, Video

Research Data Management in Life Sciences https://tess.elixir-europe.org/materials/research-data-management-in-life-sciences The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences. Data management Life Science Researchers
Alternate Representations of R Objects or ALTREP

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Alternate Representations of R Objects or ALTREP https://tess.elixir-europe.org/materials/alternate-representations-of-r-objects-or-altrep Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics https://tess.elixir-europe.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
SPARQLing Biology: a beginners course

Course given at BioSB 2019 for biologists about SPARQL.

Scientific topics: Biology

Operations: Query and retrieval

Keywords: Sparql queries, Sparql syntax

Resource type: Tutorial

SPARQLing Biology: a beginners course https://tess.elixir-europe.org/materials/sparqling-biology-a-beginners-course Course given at BioSB 2019 for biologists about SPARQL. Biology Sparql queries, Sparql syntax Biologists Chemists
Presentation on sparseMatrixStats

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Presentation on sparseMatrixStats https://tess.elixir-europe.org/materials/presentation-on-sparsematrixstats Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
runBioSimulations tutorial and help

runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL

Resource type: Tutorial, Documentation

runBioSimulations tutorial and help https://tess.elixir-europe.org/materials/runbiosimulations-tutorial-and-help runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities. The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects. Ion Moraru Bilal Shaikh Gnaneswara Marupilla Simulation experiment Computational biology Systems biology biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL modelers
BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help https://tess.elixir-europe.org/materials/biosimulators-help BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. The BioSimulators help describes how to use this registry: - How to find a containerized simulation tools that are capable of executing a modeling study. - How to use containerized simulation tools to execute modeling studies. - How to containerize a simulation tool and submit it to the BioSimulators registry. Ion Moraru Bilal Shaikh Simulation experiment Computational biology Systems biology Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL modelers Computational biologists software developers, bioinformaticians
Use Scholia and Wikidata to find scientific literature

Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others...

Keywords: Literature

Resource type: Tutorial

Use Scholia and Wikidata to find scientific literature https://tess.elixir-europe.org/materials/use-scholia-and-wikidata-to-find-scientific-literature Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others when finding literature. Proper annotation also makes scientific literature more findable. Literature Researchers
Bacterial Bioinformatics

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center,...

Keywords: life-sciences, health-informatics, research

Bacterial Bioinformatics https://tess.elixir-europe.org/materials/bacterial-bioinformatics This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow. life-sciences, health-informatics, research
Q&A about upcoming release

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Q&A about upcoming release https://tess.elixir-europe.org/materials/q-a-about-upcoming-release Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Presentation on AnVIL

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Presentation on AnVIL https://tess.elixir-europe.org/materials/presentation-on-anvil Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Data Management and Writing a Data Management Plan

Writing a Data Management Plan A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data.

Scientific topics: Data management

Resource type: e-learning

Data Management and Writing a Data Management Plan https://tess.elixir-europe.org/materials/data-management-and-writing-a-data-management-plan Writing a Data Management Plan A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data. Geert Bonamie Data management
Scop3P

Scop3P is available as a web-interface for PTM visualisation and can be accessed at https://iomics.ugent.be/scop3p Search Scop3P with Swiss-Prot accession/ID, protein name, PDB ID, ProteomeXchange ID or by keywords

Scop3P https://tess.elixir-europe.org/materials/scop3p Scop3P is available as a web-interface for PTM visualisation and can be accessed at https://iomics.ugent.be/scop3p Search Scop3P with Swiss-Prot accession/ID, protein name, PDB ID, ProteomeXchange ID or by keywords
New builder update

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

New builder update https://tess.elixir-europe.org/materials/new-builder-update Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Compiling the OSCA book on the Bioconductor build system

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Compiling the OSCA book on the Bioconductor build system https://tess.elixir-europe.org/materials/compiling-the-osca-book-on-the-bioconductor-build-system Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Browsing and searching the Bioconductor codebase

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Browsing and searching the Bioconductor codebase https://tess.elixir-europe.org/materials/browsing-and-searching-the-bioconductor-codebase Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Introduction https://tess.elixir-europe.org/materials/introduction-e309609e-264f-4023-9485-f406549bb597 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Outreach

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Outreach https://tess.elixir-europe.org/materials/outreach Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.